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Add functional specification (416 items) and link it from plan/docs

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SIMURGARRAY_FUNCTIONAL_SPEC.md defines externally visible behaviour:
CLI, inputs, genotyping outputs, QC and report, cytogenetics CNV/LOH,
targeted PGx copy number, star alleles, methylation control QC, edge-case
catalogue, performance targets, open questions and a traceability table.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
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kemalandClaude Opus 5.5 committed 2026-09-27 16:13:40 +01:00
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CLAUDE.md
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# SimurgArray
Personal research toolkit for Illumina Infinium genotyping arrays (IDAT→GTC→VCF, QC, CN, PGx).
The full spec and roadmap is SIMURGARRAY_MASTER_PLAN.md — read the relevant section before changing code.
Externally visible behaviour (CLI options, file schemas, QC semantics, messages, edge cases) is defined item-by-item
in SIMURGARRAY_FUNCTIONAL_SPEC.md (IDs like CLI-021, OUT-031); cite item IDs in commits and tests.
## Rules
- Work phase by phase (§18). Don't start a phase until the previous gate passes.